...In Sigil 0.4 this is changed. By default the opf and ncx files are kept and not overwritten. That is great if you just want to edit an epub and want to keep the structure intact (including TOC). However, if you do more than that and the TOC will change, you have two choices. Edit the ncx of opf yourself to make it correspond to the rest of the epub or recreate TOC. That will change/recreate the ncx and opf again.

So basically, you have the choice. It is not a bug, it is by deliberate design.

That will be great since for me I often only need to edit a page or add something that shouldn't change the TOC.

That said, if I do have a TOC already and want to keep it, wouldn't it seem more reasonable to have Sigil use the existing TOC and give the option to wipe/recreate it only if the user wants that? In my experience, once a TOC is built and working, I'd much rather keep and tweak it, or be able to simply add to it, before I'd ever want to just wipe it and start over. So even if something required a change to the TOC, the option to edit or add to the existing TOC seems like a more prudent option than being forced to start from scratch. But I usually keep a copy of the toc.ncx and after I've saved things I simply unzip the epub file and replace the empty Sigil one with my original. It works...no worries.
-JTT